rs2565666

chr12-19397902-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.899 in 151,976 control chromosomes in the GnomAD database, including 61,382 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.90 (61382 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136466 AN: 151858 Hom.: 61336 Cov.: 29

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.830

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.887

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.899 AC: 136573 AN: 151976 Hom.: 61382 Cov.: 29 AF XY: 0.901 AC XY: 66927 AN XY: 74284

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.917

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.888

Alfa AF: 0.896 Hom.: 12670

Bravo AF: 0.901

Asia WGS AF: 0.934 AC: 3249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.2
Dann	Benign	0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2565666; hg19: chr12-19550836;